λ噬菌体溶源/裂解转换调控与定态熵

冯维; 丁辉; 林昊; 罗辽复

doi:10.7498/aps.61.168701

摘要

被λ噬菌体感染的大肠杆菌是研究生物基因调控网络的重要模板之一. 根据该调控系统操纵子与调控蛋白相互作用特点, 利用热力学配分函数描述调控蛋白与操纵子的结合概率, 在给出该调控系统的动力学分岔的基础上, 计算系统各定态的热力学熵. 结果显示, 溶源态和裂解态较鞍点和分岔点具有更低的熵值, 且溶源态的熵最低, 说明处于溶源态的系统具有更高的生物序.

关键词:

λ 噬菌体 /
溶源/裂解转变 /
分岔 /
熵

The system of Escherichia coli infected by λ phage is one of the templates for quantitative study of regulated networks. In this article, according to the characteristics of the interactions between operators and regulators, the probabilities of regulators binding to operators are described by thermodynamic partition function. On the basis of bifurcation analysis of this regulated network, the entropies of stationary states are calculated. Results show that the entropies of both lysogenic state and lytic state are lower than those of saddle-point and bifurcation point states. Moreover, we find that the lysogenic state has lower entropy than lytic state, which proves that the lysogenic state has a higher biological order.

Keywords:

作者及机构信息

1.
电子科技大学生命科学与技术学院, 神经信息教育部重点实验室, 生物信息中心, 成都 610054;

2.
内蒙古大学物理科学与技术学院, 理论生物物理实验室, 呼和浩特 010021

基金项目: 国家自然科学基金(批准号: 11047180, 90403010, 200408020102)和电子科技大学科研启动经费资助的课题.

Authors and contacts

1.
Key Laboratory for Neuro Information of Ministry of Education, Center of Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China;

2.
Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China

Funds: Project supported by the National Natural Science Foundation of China (Grant Nos. 11047180, 90403010, 200408020102) and the Scientific Research Startup Foundation of University of Electronic Science and Technology of China.

参考文献

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[2]	Ackers G K, Johnson A D, Shea M A 1982 Proc. Natl. Acad. Sci. U. S. A. 79 1129
[3]	Shea M A, Ackers G K 1985 J. Mol. Biol. 181 211
[4]	Yi M, Jia Y, Liu Q, Zhan X 2008 Acta Phys. Sin. 57 621 (in Chinese) [易鸣, 贾亚, 刘泉, 詹璇 2008 57 621]
[5]	Aurell E, Brown S, Johanson J, Sneppen K 2002 Phys. Rev. E 65 051914
[6]	Santillan M, Mackey M C 2004 Biophys. J. 86 75
[7]	Wan X, Zhou J, Liu Z R 2012 Acta Phys. Sin. 61 010203 (in Chinese) [万茜, 周进, 刘曾荣 2012 61 010203]
[8]	Bakk A, Metzler R, Sneppen K 2004 Biophys. J. 86 58
[9]	McAdams H H, Shapiro L 1995 Science 269 650
[10]	Aurell E, Sneppen K 2002 Phys. Rev. Lett. 88 048101
[11]	Tian T, Burrage K 2004 J. Theor. Biol. 227 229
[12]	Liu S B, Wu Y, Hao Z W, Li Y J, Jia N 2012 Acta Phys. Sin. 61 020503 (in Chinese) [刘少宝, 吴莹, 郝忠文, 李银军, 贾宁 2012 61 020503]
[13]	Li R, Yan P L, Chen J, Li J, Li J, Zhang K W, Zhong J X 2009 Acta Phys. Sin. 58 6703 (in Chinese) [李蓉, 颜平兰, 陈健, 李俊, 李金, 张凯旺, 钟建新 2009 58 6703]
[14]	Zhu X M, Yin L, Hood L, Ao P 2004 Funct. Integr. Genomics 4 188
[15]	Lou C B, Yang X J, Liu X L, He B, Ouyang Q 2007 Biophys. J. 92 2685
[16]	Wang S Y, Zhang Y P, Ouyang Q 2006 Phys. Rev. E 73 041922
[17]	Gedeon T, Mischaikow K, Patterson K, Traldi E 2008 Biophys. J. 94 3384
[18]	Morelli M J, Wolde P R, Allen R J 2009 Proc. Natl. Acad. Sci. U. S. A. 106 8101
[19]	Werner M, Aurell E 2009 Phys. Biol. 6 046007
[20]	Avlund M, Krishna S, Semsey S, Dodd I B, Sneppen K 2010 PLoS One 5 e15037
[21]	Cao Y, Lu H M, Liang J 2010 Proc. Natl. Acad. Sci. U. S. A. 107 18445
[22]	Joh R I, Weitz J S 2011 PLOS Comput. Biol. 7 e1002006
[23]	Nicolis G, Prigogine I 1977 Self-Organization in Nonequilibrium Systems (New York: Wiley Publishing)
[24]	Lehninger A L 1982 Principles of Biochemistry (Delhi: CBS Publishers and Distributors)
[25]	Ding H, Luo L 2009 Chin. Phys. Lett. 26 098701
[26]	Ding H, Luo L F, Lin H 2011 Commun. Theor. Phys. 55 371
[27]	Luo L F 2009 Front. Phys. China 4 122
[28]	Stoll G, Rougemont J, Naef F 2006 Bioinformatics 22 2539
[29]	Schrödinger E 1945 What is Life? (Cambridge: Cambridge University Press) p24
[30]	Luo L F 2010 Sci. Tech. Rev. 28 106 (in Chinese) [罗辽复 2010 科技导报 28 106]

施引文献

[1]	Arkin A, Ross J, McAdams H H 1998 Genetics 149 1633
[2]	Ackers G K, Johnson A D, Shea M A 1982 Proc. Natl. Acad. Sci. U. S. A. 79 1129
[3]	Shea M A, Ackers G K 1985 J. Mol. Biol. 181 211
[4]	Yi M, Jia Y, Liu Q, Zhan X 2008 Acta Phys. Sin. 57 621 (in Chinese) [易鸣, 贾亚, 刘泉, 詹璇 2008 57 621]
[5]	Aurell E, Brown S, Johanson J, Sneppen K 2002 Phys. Rev. E 65 051914
[6]	Santillan M, Mackey M C 2004 Biophys. J. 86 75
[7]	Wan X, Zhou J, Liu Z R 2012 Acta Phys. Sin. 61 010203 (in Chinese) [万茜, 周进, 刘曾荣 2012 61 010203]
[8]	Bakk A, Metzler R, Sneppen K 2004 Biophys. J. 86 58
[9]	McAdams H H, Shapiro L 1995 Science 269 650
[10]	Aurell E, Sneppen K 2002 Phys. Rev. Lett. 88 048101
[11]	Tian T, Burrage K 2004 J. Theor. Biol. 227 229
[12]	Liu S B, Wu Y, Hao Z W, Li Y J, Jia N 2012 Acta Phys. Sin. 61 020503 (in Chinese) [刘少宝, 吴莹, 郝忠文, 李银军, 贾宁 2012 61 020503]
[13]	Li R, Yan P L, Chen J, Li J, Li J, Zhang K W, Zhong J X 2009 Acta Phys. Sin. 58 6703 (in Chinese) [李蓉, 颜平兰, 陈健, 李俊, 李金, 张凯旺, 钟建新 2009 58 6703]
[14]	Zhu X M, Yin L, Hood L, Ao P 2004 Funct. Integr. Genomics 4 188
[15]	Lou C B, Yang X J, Liu X L, He B, Ouyang Q 2007 Biophys. J. 92 2685
[16]	Wang S Y, Zhang Y P, Ouyang Q 2006 Phys. Rev. E 73 041922
[17]	Gedeon T, Mischaikow K, Patterson K, Traldi E 2008 Biophys. J. 94 3384
[18]	Morelli M J, Wolde P R, Allen R J 2009 Proc. Natl. Acad. Sci. U. S. A. 106 8101
[19]	Werner M, Aurell E 2009 Phys. Biol. 6 046007
[20]	Avlund M, Krishna S, Semsey S, Dodd I B, Sneppen K 2010 PLoS One 5 e15037
[21]	Cao Y, Lu H M, Liang J 2010 Proc. Natl. Acad. Sci. U. S. A. 107 18445
[22]	Joh R I, Weitz J S 2011 PLOS Comput. Biol. 7 e1002006
[23]	Nicolis G, Prigogine I 1977 Self-Organization in Nonequilibrium Systems (New York: Wiley Publishing)
[24]	Lehninger A L 1982 Principles of Biochemistry (Delhi: CBS Publishers and Distributors)
[25]	Ding H, Luo L 2009 Chin. Phys. Lett. 26 098701
[26]	Ding H, Luo L F, Lin H 2011 Commun. Theor. Phys. 55 371
[27]	Luo L F 2009 Front. Phys. China 4 122
[28]	Stoll G, Rougemont J, Naef F 2006 Bioinformatics 22 2539
[29]	Schrödinger E 1945 What is Life? (Cambridge: Cambridge University Press) p24
[30]	Luo L F 2010 Sci. Tech. Rev. 28 106 (in Chinese) [罗辽复 2010 科技导报 28 106]

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